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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Modeling Infectious Disease Agents Study online portal for COVID-19 Resource Report Resource Website 1+ mentions |
Modeling Infectious Disease Agents Study online portal for COVID-19 (RRID:SCR_018281) | data or information resource, portal, topical portal | Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases. | COVID-19, COVID-19 data, modeling research, public data, metadata, infectious disease | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | NIGMS | Free, Freely available | https://github.com/midas-network/COVID-19 | SCR_018281 | MIDAS online portal for COVID-19 | 2026-09-12 12:58:59 | 4 | ||||||
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Recombination Detection Program Resource Report Resource Website 500+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | data analysis software, data processing software, software application, software resource | Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes. | DNA sequence, alignment, phylogenetic tree, nucleotide analysis, sequence data analysis, genetic recombination identification, DNA sequence alignment, recombinant pattern analysis, virus genome | Carnergie Corporation ; European Research Council ; Fund for Scientific Research Flanders ; NIAID AI090970; NIAID AI100665; NIGMS U01 GM110749; Polyomielitis Research Foundation ; South African Centre of High Performance Computing ; South African National Research Foundation ; Spanish Ministry of Science and Education ; University of Cape Town ; Wellcome Trust |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-09-12 12:59:02 | 507 | |||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | data access protocol, software resource, software toolkit, web service | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-09-12 12:59:04 | 0 | ||||||
|
Datanator Resource Report Resource Website 1+ mentions |
Datanator (RRID:SCR_018651) | application programming interface, data access protocol, data or information resource, database, software resource, web application | Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition. | Data discovering, cell model, model cellular biochemistry, modeling specific organism, specific environmental condition, genomics, proteomics, epigenomics, metabolomics, system biology, bio.tools |
uses: BpForms is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIBIB P41 EB023912; NIGMS R35 GM119771 |
DOI:10.1101/2020.08.06.240051 | Free, Freely available | biotools:datanator, r3d100013339 | https://github.com/karrlab/datanator, https://bio.tools/datanator, https://doi.org/10.17616/R31NJMSB | SCR_018651 | 2026-09-12 12:59:04 | 2 | ||||||
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Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
DOE CSGF fellowship ; NIGMS R01 GM106303; NSF GRFP DGE1144152 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | EVcouplings | 2026-09-12 12:59:05 | 26 | |||||
|
DE-Sim Resource Report Resource Website |
DE-Sim (RRID:SCR_018770) | simulation software, software application, software resource | Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models. | Object oriented, discrete event simulation, data driven modeling, oriented discrete event simulation, computation model simulation |
is related to: NumPy is related to: SciPy is related to: Pandas is related to: SIMULA has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Icahn Institute for Data Science and Genomic Technology ; NIGMS R35 GM119771; NSF 1649014 |
Free, Available for download, Freely available | SCR_018770 | Discrete Event Simulation, object oriented Discrete Event-Simulation tool | 2026-09-12 12:59:05 | 0 | ||||||||
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RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, data processing software, software application, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
Berlin Institute for Medical Systems Biology ; NIGMS R01 GM104962 |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-09-12 12:59:06 | 8 | ||||||
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CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI R00 HG008399; NHGRI R01 HG005085; NHGRI RM1 HG009490; NHLBI P01 HL32262; NHLBI R01 HL119099; NIBIB R01 EB022376; NIDDK P30 DK049216; NIDDK R03 DK109232; NIGMS R35 GM118062; NIGMS R35 GM118158 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2, https://github.com/pinellolab/CRISPResso | SCR_021538 | CRISPResso2 | 2026-09-12 12:59:57 | 27 | |||||||
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RepEnrich Resource Report Resource Website 10+ mentions |
RepEnrich (RRID:SCR_021733) | data analysis software, data processing software, software application, software resource | Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data. | profile enrichment, next generation sequencing reads, transposable elements, estimate repetitive element enrichment, genome wide transcriptional regulation, sequencing data | has parent organization: Brown University; Rhode Island; USA | NIA K25 AG028753; NIA R37 AG016694; NIGMS T32 GM007601 |
PMID:25012247 | Free, Available for download, Freely available | https://github.com/nerettilab/RepEnrich2 | SCR_021733 | RepEnrich2 | 2026-09-12 01:00:00 | 21 | ||||||
|
DeepCell Resource Report Resource Website 10+ mentions |
DeepCell (RRID:SCR_022197) | data processing software, image analysis software, segmentation software, software application, software resource | Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software. | segmenting individual cells, microscopy image, cell segmentation | NIGMS F32 GM119319; NIGMS P50 GM107615; NLM DP1 LM01150; Paul Allen Family Foundation |
DOI:10.1371/journal.pcbi.1005177 | Free, Available for download, Freely available | SCR_022197 | Deepcell | 2026-09-12 01:00:06 | 14 | ||||||||
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SCIRun Resource Report Resource Website 10+ mentions |
SCIRun (RRID:SCR_002541) | SCIRun | data processing software, data visualization software, simulation software, software application, software resource, software toolkit | A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6. | modeling, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BioMesh3D is related to: BioMesh3D is related to: BioPSE is related to: BioPSE has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Free, Available for download, Freely available | nlx_155949 | http://www.nitrc.org/projects/scirun | SCR_002541 | 2026-09-12 01:00:08 | 22 | ||||||
|
ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NIGMS RC2 GM092519; NIH ; NIMH ; NINDS ; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; Wellcome Trust Strategic Award 095931 |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, SCR_018407, nif-0000-30467 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-09-12 01:00:09 | 29025 | ||||
|
ToRNADo Resource Report Resource Website 100+ mentions |
ToRNADo (RRID:SCR_002706) | data processing software, data visualization software, software application, software resource | A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion. | duplex, protein, rna, visualization | has parent organization: Stanford University; Stanford; California | NIH ; NIGMS R01GM107340; NIGMS U54GM072970 |
Free, Available for download, Freely available | nif-0000-23335 | SCR_002706 | 2026-09-12 01:00:08 | 105 | ||||||||
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TFmodeller Resource Report Resource Website 1+ mentions |
TFmodeller (RRID:SCR_015715) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, web application | Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs. | protein-dna complex, comparative model, modeling software, schematic interface diagram, interface alignment, dna motif, complex coordinate | NIGMS RO1-GM071962 | PMID:17459960 | Free for academic use, Freely available, Tutorial available | http://maya.ccg.unam.mx/~tfmodell/ | SCR_015715 | 2026-09-12 12:58:29 | 1 | ||||||||
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GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | data analysis software, data processing software, software application, software resource | Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme. | GEO2Enrichr, gene expression signatures, enrichment analyses, multiple studies, biological theme, bio.tools |
is listed by: bio.tools is listed by: Debian works with: Gene Expression Omnibus (GEO) |
NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27846806 | Free, Freely available | biotools:gen3va | https://github.com/MaayanLab/gen3va, https://bio.tools/gen3va | SCR_015682 | GENE Expression and Enrichment Vector Analyzer | 2026-09-12 12:58:29 | 5 | |||||
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CRowd Extracted Expression of Differential Signatures Resource Report Resource Website 1+ mentions |
CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) | CREEDS | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures. | variant, disease expression, disease marker | NIGMS R01GM098316; NHLBI U54HL127624; NCI U54CA189201 |
PMID:27667448 | Freely available, Free, Available for download | SCR_015680 | CREEDS: CRowd Extracted Expression of Differential Signatures | 2026-09-12 12:58:29 | 6 | |||||||
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NeuroExpresso Resource Report Resource Website 10+ mentions |
NeuroExpresso (RRID:SCR_015724) | data or information resource, database, software resource, web application | Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. | mouse brain, marker gene, tissue expression, microarray, gene expression, rna sequencing | NeuroDevNet ; CAMH ; NIMH MH077159; NIMH MH111099; NIGMS 719GM076990; NSERC Discovery Grant |
Freely available | https://github.com/oganm/neuroexpresso | SCR_015724 | 2026-09-12 12:58:29 | 26 | |||||||||
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Rosetta Resource Report Resource Website 100+ mentions |
Rosetta (RRID:SCR_015701) | simulation software, software application, software resource, software toolkit | Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Molecular modeling, structure prediction, computational modeling, protein analysis, enzyme design, macromolecular complexes |
is used by: trRosetta is related to: PyRosetta works with: ROSIE |
Hertz Foundation Fellowship ; NCI F32 CA189246; NIGMS GM078221; NIGMS GM084453; NIGMS GM092802; NIGMS GM110089; NIGMS GM111819; NIGMS GM114961; NIGMS GM117189; NIGMS GM73141; NSF Graduate Research Fellowship ; NSF BMAT 1507736; Simons Foundation |
PMID:28430426 PMID:21829626 PMID:18442991 |
Restricted | SCR_015701 | Rosetta modeling software | 2026-09-12 12:58:29 | 216 | |||||||
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Edtsurf Resource Report Resource Website 1+ mentions |
Edtsurf (RRID:SCR_016083) | data processing software, data visualization software, software application, software resource, source code | Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening. | construct, triangulate, surface, macromolecule, van der Waals, solvent, accessible, molecular, cavities, program |
is listed by: Debian is listed by: OMICtools |
NIGMS GM083107; NIGMS GM084222; NSF 0746198; the Alfred P. Sloan Foundation |
PMID:19956577 | Free, Available for download, Freely available | OMICS_16795 | https://sources.debian.org/src/edtsurf/ | SCR_016083 | EDTSurf: Quick and accurate construction of macromolecular surfaces | 2026-09-12 12:58:35 | 4 | |||||
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PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data analysis software, data processing software, software application, software resource | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | Carver Chair in Molecular Medicine ; Fraternal Order of Eagles Diabetes Research Center ; NHLBI R24 HL123482; NIDDK R01 DK115791; NIDDK R24 DK096518; NIGMS T32 GM082729; University of Iowa Center for Gene Therapy |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | 2026-09-12 12:58:46 | 5 |
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